| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Celiac_Disease" | |
| # Input paths | |
| tcga_root_dir = "../DATA/TCGA" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Celiac_Disease/TCGA.csv" | |
| out_gene_data_file = "./output/preprocess/3/Celiac_Disease/gene_data/TCGA.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Celiac_Disease/clinical_data/TCGA.csv" | |
| json_path = "./output/preprocess/3/Celiac_Disease/cohort_info.json" | |
| # Check available directories | |
| available_dirs = os.listdir(tcga_root_dir) | |
| available_dirs = [d for d in available_dirs if not d.startswith('.') and not d.endswith('.ipynb')] | |
| # For cardiovascular disease, there is no directly matching cohort in TCGA | |
| # Mark the trait as not available and exit | |
| is_usable = validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort="TCGA", | |
| info_path=json_path, | |
| is_gene_available=False, | |
| is_trait_available=False | |
| ) | |
| raise ValueError(f"No suitable TCGA cohort found for {trait}") |